Yes I know exactly what you mean. I tried syncing my Kobo with Calibre and the folders were transferred. I deleted them and just copied the epubs to the reader. Not too certain if epubs would have shown in reader library as they were tucked inside authors folders. With Calibre being such a sophisticated app I would be surprised if there wasn't a way round this. I've yet to find it though.
Edit: After reading the thread mentioned by theducks I will comment no further on this subject as public flagellation does not appeal to me.

Last edited by Wordsworth; 02-04-2013 at 12:27 PM.
Reason: Afterthought